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Aims To quantify thoracic lymphatic burden in paediatric Fontan patients using MRI and correlate with clinical status. Methods and results Paediatric Fontan patients (<18-years-old) with clinical cardiac MRI that had routine lymphatic 3D T2 fast spin echo (FSE) imaging performed from May 2017 to October 2019 were included. 'Lymphatic burden' was quantified by thresholding-based segmentation of the 3D T2 FSE maximum intensity projection image and indexed to body surface area, performed by two independent readers blinded to patient status. There were 48 patients (27 males) with median age at MRI of 12.9 (9.4–14.7) years, time from Fontan surgery to MRI of 9.1 (5.9–10.4) years, and follow-up time post-Fontan surgery of 9.4 (6.6–11.0) years. Intraclass correlation coefficient between two observers for lymphatic burden was 0.96 (0.94–0.98). Greater lymphatic burden correlated with post-Fontan operation hospital length of stay and duration of chest tube drainage (r s = 0.416, P = 0.004 and r s = 0.439, P = 0.002). Median lymphatic burden was greater in patients with chylous effusions immediately post-Fontan (178 (118–393) vs. 113 (46–190) mL/m2, P = 0.028), and in patients with composite adverse Fontan status (n = 13) defined by heart failure (n = 3), transplant assessment (n = 2), recurrent effusions (n = 6), Fontan thrombus (n = 2), and/or PLE (n = 6) post-Fontan (435 (137–822) vs. 114 (51–178) mL/m2, P = 0.003). Lymphatic burden > 600 mL/m2 was associated with late adverse Fontan status with sensitivity of 57% and specificity of 95%. Conclusion Quantification of MR lymphatic burden is a reliable tool to assess the lymphatics post-Fontan and is associated with clinical status. [ABSTRACT FROM AUTHOR]